It is not difficult to keep positive standings (all above zero) with all the Empire factions simultaneously, even if running only normal missions.With good forethought you can avoid the horrible grinding mess that it can be to recover extremely low faction standings. Do not kill faction ships (decline those missions), and have a way to balance the effects of storylines once in a while. If you do want to keep faction standings balanced, the best way is to not let them drop in the first place.
There are some benefits to this (freedom of travel mainly), which must be weighed against the rewards of achieving excellent standing with one faction.
The exception to this is R&D agents: if you attempt to use your faction standing to access an R&D agent, you must also have the appropriate corp standing up to the agent's requirement -2. That means, even if you have no corp standing with Caldari Navy, if you have faction standing with the Caldari State then you will be able to access agents using that faction standing. Most agents will accept either faction, corp, or personal standing to fulfill their requirement.
Unmodified faction standing of 0.0 or higher is also requirement for joining the faction warfare. This includes normal agents, COSMOS agents and epic arc agents (元 for pirate epic arcs, L4 for empire epic arcs). Faction standing gives access to agents from all corporations belonging to that factions. Faction standing is the strongest NPC standing.